title: Serotype-specific identification of polioviruses by PCR using primers containing mixed-base or deoxyinosine residues at positions of codon degeneracy.
abstract: We have developed a method for determining the serotypes of poliovirus isolates by PCR. Three sets of serotype-specific antisense PCR-initiating primers (primers seroPV1A, seroPV2A, and seroPV3A) were designed to pair with codons of VP1 amino acid sequences that are conserved within but that differ across serotypes. The sense polarity primers (primers seroPV1S, seroPV2S, and seroPV3S) matched codons of more conserved capsid sequences. The primers contain mixed-base and deoxyinosine residues to compensate for the high rate of degeneracy of the targeted codons. The serotypes of all polioviruses tested (48 vaccine-related isolates and 110 diverse wild isolates) were correctly identified by PCR with the serotype-specific primers. None of the genomic sequences of 49 nonpolio enterovirus reference strains were amplified under equivalent reaction conditions with any of the three primer sets. These primers are useful for the rapid screening of poliovirus isolates and for determining the compositions of cultures containing mixtures of poliovirus serotypes.
authors.affiliation: Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA. dyk0@cdc.gov
authors.forename: D R
authors.initials: DR
authors.lastname: Kilpatrick
authors.forename: B
authors.initials: B
authors.lastname: Nottay
authors.forename: C F
authors.initials: CF
authors.lastname: Yang
authors.forename: S J
authors.initials: SJ
authors.lastname: Yang
authors.forename: E
authors.initials: E
authors.lastname: Da Silva
authors.forename: S
authors.initials: S
authors.lastname: Peñaranda
authors.forename: M
authors.initials: M
authors.lastname: Pallansch
authors.forename: O
authors.initials: O
authors.lastname: Kew
mesh_terms: D000595:Amino Acid Sequence; D016375:Antisense Elements (Genetics); D002213:Capsid / Q000235:genetics / Q000276:immunology; D036022:Capsid Proteins; D003062:Codon; D006801:Humans; D008969:Molecular Sequence Data; D011051:Poliomyelitis / Q000276:immunology; D017955:Poliovirus / Q000145:classification* / Q000235:genetics* / Q000276:immunology; D011054:Poliovirus Vaccine, Inactivated / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000379:methods*; D012367:RNA, Viral / Q000032:analysis / Q000235:genetics; D017423:Sequence Analysis, RNA; D012703:Serotyping; D014407:Tumor Cells, Cultured
chemical_list: D016375:Antisense Elements (Genetics); D036022:Capsid Proteins; D003062:Codon; D011054:Poliovirus Vaccine, Inactivated; D012367:RNA, Viral; C442540:VP1 protein, Poliovirus